In this particular script, the Si atom in the corner with smallest XYZ coordinates is not hydrogenated properly. Maybe there are others too, I just noticed that one since it's easy to spot. This creates a dangling bond which may change the electronic structure, at least a little bit.
There is no limitation in the software that makes certain sizes of system behave differently. However, depending on the computational parameters or model used, the results may of course vary to other studies.